Appending hotkeys to default keymap
Perhaps you could apply the keymap after startup as an addon, rather than in the startup folder?
Here is an extract of an example script from an addon I wrote to Toggle Emulate MMB &amp; Numpad. I have included some keymap reference documentation in the repository, and commented code that might make it easier for you to set up your own script. I have removed here the superfluous elements for your purposes.
bl_info = {
    &quot;name&quot;: &quot;My Custom Keymaps&quot;,
    &quot;author&quot;: &quot;me&quot;,
    &quot;version&quot;: (1, 0),
    &quot;blender&quot;: (2, 90, 1),
    &quot;location&quot;: &quot;...&quot;,
    &quot;description&quot;: &quot;Loading Custom Keymaps&quot;,
    &quot;warning&quot;: &quot;&quot;,
    &quot;wiki_url&quot;: &quot;&quot;,
    &quot;category&quot;: &quot;Preferences&quot;}

import bpy
import rna_keymap_ui
from bpy.utils import register_class, unregister_class

# Keymap Code

# First, set up a dictionary of key mappings.

# &quot;TEMPLATE&quot;: [{&quot;label&quot;: &quot;Human readable name of keymap in Blender Keymap UI&quot;,
#               &quot;region_type&quot;: &quot;WINDOW&quot;, //Default is WINDOW (optional)
#               &quot;space_type&quot;, &quot;EMPTY&quot;, //Default is EMPTY
#               &quot;map_type&quot;: &quot;KEYBOARD&quot;, //Device to be used (optional)
#               &quot;keymap&quot;: &quot;Window&quot;, //Name to be chosen from declared list of keymap names
#               &quot;idname&quot;: ..., //Specific reference to operator from blender API
#               &quot;type&quot;: &quot;&quot;, //Key type identifier - choose a specific keyboard button or mouse button, etc...
#               &quot;ctrl&quot;: False, //Combination keys for compound hotkeys (optional)
#               ...
#               &quot;value&quot;: &quot;PRESS&quot;}, //Whether key will be held, pressed, etc...
#              {...}]

keys = {&quot;MENU&quot;: [{&quot;label&quot;: &quot;Toggle Emulate 3 Button Mouse&quot;,
                  &quot;region_type&quot;: &quot;WINDOW&quot;,
                  &quot;space_type&quot;: &quot;EMPTY&quot;,
                  &quot;map_type&quot;: &quot;KEYBOARD&quot;,
                  &quot;keymap&quot;: &quot;Window&quot;,
                  &quot;idname&quot;: &quot;preferences.toggle_emulate_3_button_mouse&quot;,
                  &quot;type&quot;: &quot;QUOTE&quot;,
                  &quot;ctrl&quot;: False,
                  &quot;alt&quot;: False,
                  &quot;shift&quot;: False,
                  &quot;oskey&quot;: False,
                  &quot;value&quot;: &quot;PRESS&quot;
                  },
                {&quot;label&quot;: &quot;Toggle Emulate Numpad&quot;,
                  &quot;region_type&quot;: &quot;WINDOW&quot;,
                  &quot;space_type&quot;: &quot;EMPTY&quot;,
                  &quot;map_type&quot;: &quot;KEYBOARD&quot;,
                  &quot;keymap&quot;: &quot;Window&quot;,
                  &quot;idname&quot;: &quot;preferences.toggle_numpad&quot;,
                  &quot;type&quot;: &quot;SEMI_COLON&quot;,
                  &quot;ctrl&quot;: False,
                  &quot;alt&quot;: False,
                  &quot;shift&quot;: False,
                  &quot;oskey&quot;: False,
                  &quot;value&quot;: &quot;PRESS&quot;
                  }]}

# Define a function to get a list of key mappings, 'keylists'
def get_keys():
    keylists = []
    keylists.append(keys[&quot;MENU&quot;])
    return keylists

# Define a function to register the key mappings templated in the dict as keymaps, using the constructor kc.keymaps.new()        
def register_keymaps(keylists):
    wm = bpy.context.window_manager
    kc = wm.keyconfigs.addon

    keymaps = []

    for keylist in keylists:
        for item in keylist:
            keymap = item.get(&quot;keymap&quot;)
            space_type = item.get(&quot;space_type&quot;, &quot;EMPTY&quot;)
            region_type = item.get(&quot;region_type&quot;, &quot;WINDOW&quot;)

            if keymap:
                km = kc.keymaps.new(name=keymap, space_type=space_type, region_type=region_type)
                # km = kc.keymaps.new(name=keymap, space_type=space_type)

                if km:
                    idname = item.get(&quot;idname&quot;)
                    type = item.get(&quot;type&quot;)
                    value = item.get(&quot;value&quot;)

                    shift = item.get(&quot;shift&quot;, False)
                    ctrl = item.get(&quot;ctrl&quot;, False)
                    alt = item.get(&quot;alt&quot;, False)
                    oskey = item.get(&quot;oskey&quot;, False)

                    kmi = km.keymap_items.new(idname, type, value, shift=shift, ctrl=ctrl, alt=alt, oskey=oskey)

                    if kmi:
                        properties = item.get(&quot;properties&quot;)

                        if properties:
                            for name, value in properties:
                                setattr(kmi.properties, name, value)

                        keymaps.append((km, kmi))
    return keymaps

# Define a function to unregister the keymaps
def unregister_keymaps(keymaps):
    for km, kmi in keymaps:
        km.keymap_items.remove(kmi)


def register():
    global keymaps
    keys = get_keys()
    keymaps = register_keymaps(keys)




def unregister():
    global keymaps
    for km, kmi in keymaps:
        km.keymap_items.remove(kmi)